President Obama introduced Janet Napolitano to the nation five years ago as a tough-minded border-state governor uniquely suited to fixing illegal immigration. “She knows firsthand the need to have a partner in Washington that works well with state and local governments. She understands as well as anyone the danger of an unsecure border,” he said.

But on Friday, Homeland Security Secretary Napolitano bid farewell to the national stage to become president of the University of California system, with her work on the border incomplete and new funding for border security still trapped in political fights over comprehensive immigration reform.

That is not to say she did not make progress. The Congressional Research Service estimates that total annual illegal inflows across the southern border fell from between 760,000 and 1.4 million in 2004 to between 340,000 and 580,000 annually in 2009 and 2010. In 2012, there was an estimated uptick to between 400,000 and 660,000 illegal crossings, a statistic that shows the responsiveness of immigration trends to economic trends in the United States. The rate of deportations under Napolitano has also risen steadily, from 389,834 in 2009 to 409,849 in 2012. As a result, the Obama Administration has already deported in five years as many people a George W. Bush deported over two terms in office.

To do more, Napolitano had long argued that she needed new funding to increase security on the border. “When it comes to immigration, I took an oath as Secretary of Homeland Security to secure the nation by enforcing the law and managing legal flows across the border,” Napolitano said in November of 2009. “Let me be clear: to do this job as effectively as possible, DHS needs immigration reform.” Indeed, the Congressional Budget Office estimates that the recent Senate-passed immigration bill would further decrease illegal entries to the United States by between 33% and 50% compared with current efforts.

But political divisions have frustrated that hope, with Republicans in the House now rejecting the Senate effort. The terms of the Senate deal could also make confirming a replacement for Napolitano more complicated. Under the Senate bill, the Director of Homeland Security has significant new powers. These include developing a plan to control the border, reporting back on its progress and certifying that certain security benchmarks—such as 90% apprehension rates for illegal crossings—have been met after five years.

In a sign of Republican distrust that Napolitano or her successor would carry out those duties, Kentucky Senator Rand Paul proposed an amendment, dubbed “Trust but Verify,” which would have instead required Congress to certify that the border was secure before immigrants were granted legal status. Leery that partisan politics would disrupt immigration reform, the Senate voted to table Paul’s amendment.

President Obama Friday praised Napolitano’s work on immigration. “Since day one, Janet has led my administration’s effort to secure our borders, deploying a historic number of resources, while also taking steps to make our immigration system fairer and more consistent with our values,” he said. And in her own statement, Napolitano noted the work she had done. “The Department has improved the safety of travelers, implemented smart steps that make our immigration system more fair and focused while deploying record resources to protect our nation’s borders,” she said.

She did not add what everyone already knows: That work is not yet done.